ATF4 p.Glu304=
c.912G>A · rs1160465011 · VCV736103
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.33 | GERP -3.7, phastCons 0.94 |
| Overall | ||
| CADD | 1.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,916 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000372%
6/1,613,730 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ATF4
- Protein
- p.Glu304=
- Coding
- c.912G>A
- MANE Select
- NM_182810
- dbSNP
- rs1160465011
- Type
- single nucleotide variant
- Location
- chr22:39522458 (GRCh38)
- Gene constraint
- LOEUF 0.718 · pLI 0.38 (gnomAD)
- Structure
- AlphaFold pLDDT 62.95 · 2 PDB
- Residue 304
- the bzip domain; an α-helix
Similar variants
- ATF4 p.Ala324Val Benign ★★ same type
- ATF4 p.Asn131= Benign ★★ same type
- ATF4 p.Glu322Asp Benign ★★ ⚠ same type
- ATF4 p.Glu3Lys Benign ★★ ⚠ same type
- ATF4 p.Ile208Met Likely benign ★★ ⚠ same type
- ATF4 p.Pro258Ala Benign ★★ same type
- ATF4 p.Thr137Ser Likely benign ★★ same type
- ATF4 p.Tyr200= Benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/atf4-p-glu304 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown